ArticleBMC plant biology2018
Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.).
Article in BMC plant biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
- Parent-of-origin effects orchestrate transcriptional reprogramming and epigenetic regulation of seedling vigor heterosis in triploid loquat.Frontiers in plant science · 2025Article
- Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines.iScience · 2023Article
- Article
- Alkaline Stress Induces Different Physiological, Hormonal and Gene Expression Responses in Diploid and Autotetraploid Rice.International journal of molecular sciences · 2022Article
- Genome-Wide Analysis, Modeling, and Identification of Amino Acid Binding Motifs Suggest the Involvement ofPlants (Basel, Switzerland) · 2021Article
- Salt stress and salt shock differently affect DNA methylation in salt-responsive genes in sugar beet and its wild, halophytic ancestor.PloS one · 2021Article
- Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat.The plant genome · 2020Article
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
backgroundPolyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants.
resultsIn our study, we used an apomictic rice line (SARII-628) that produces twin seedlings of different ploidy for methylated DNA immunoprecipitation sequencing (MeDIP-seq). We compared the level of methylation and mRNA expression in three different (CG, CHG, and CHH) sequence contexts of promoter region among haploid (1X), diploid (2X), and triploid (3X) seedling. We used MeDIP-Seq analysis of 14 genes to investigate whole genome DNA methylation and found that relative level of DNA methylation across different ploidy was in following order e.g. diploid > triploid > haploid. GO functional classification of differentially methylated genes into 9 comparisons group of promoter, intergenic and intragenic region discovered, these genes were mostly enriched for cellular component, molecular function, and biological process. By the comparison of methylome data, digital gene expression (DGE), mRNA expression profile, and Q-PCR findings LOC_ Os07g31450 and LOC_ Os01g59320 were analyzed for BS-Seq (Bisulphite sequencing).
conclusionsWe found that (1) The level of the promoter DNA methylation is negatively correlated with gene expression within each ploidy level. (2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy (from diploid to haploid, or diploid to triploid) reveals supreme changes in methylation frequency of CHH sequence context. Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice.
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